SBC logo Authors: Amine Heddad, Andrea Krings, Markus Brameier and Bob MacCallum, Stockholm Bioinformatics Center, Stockholm University, Sweden.

NucPred

Fetching Q9ERH3 from www.uniprot.org...

The NucPred score for your sequence is 0.57 (see score help below)

   1  MAGNSLVLPIVLWGRKAPTHCISSILLTDDGGTIVTGCHDGQICLWDLSE    50
  51  ELEVNPRALLFGHTAAITCLSKACASGDKQYTVSASANGEMCLWDVNDGR   100
 101  CIEFTKLACTHTGIQFYQFSVGNQREGRLLCHGHYPEILVVDATSLEVLY   150
 151  SLVSKISPDWISSMSIIRSHRTQEDTVVALSVTGILKVWIVTSEISGLQD   200
 201  TEPIFEEESKPIYCQNCQSLSFCAFTQRSLLVVCSKYWRVFDAGDYSLLC   250
 251  SGPSEDGQTWTGGDFVSADKVIIWTENGQSYIYKLPASCLPASDSFRSDV   300
 301  GKAVENLIPPVQHSLLDQKDRELVICPPVTRFFYGCKEYLHKLLIQGDSS   350
 351  GRLSIWNIADIADKQEANEGLKTTTCISLQDAFDKLKPCPAGIIDQLSVI   400
 401  PNSNEPLKVTASVYIPAHGRLVCGREDGSIIIVPATQTAIVQLLQGEHML   450
 451  RRGWPPHRTLRGHRNKVTCLLYPHQVSARYDQRYLISGGVDFSVIIWDIF   500
 501  SGEMKHIFCVHGGEITQLLVPPENCSARVQHCVCSVASDHSVGLLSLREK   550
 551  KCIMLASRHLFPIQVIKWRPSDDYLVVGCTDGSVCVWQMDTGALDRCAMG   600
 601  ITAVEILNACDEAVPAAVDSLSHPAVNLKQAMTRRSLAALKNMAHHKLQT   650
 651  LATNLLASEASDKGNLPKYSHNSLMVQAIKTNLTDPDIHVLFFDVEALII   700
 701  QLLTEEASRPNTALISPENLQKASGSSDKGGSFLTGKRAAVLFQQVKETI   750
 751  KENIKEHLLDEEEDEEEVMRQRREESDPEYRASKSKPLTLLEYNLTMDTA   800
 801  KLFMSCLHAWGLNEVLDEVCLDRLGMLKPHCTVSFGLLSRGGHMSLMLPG   850
 851  YNQAAGKLLQAKAEAGRKGPATESVGKGTYTVSRAVTTQHLLSIISLANT   900
 901  LMSMTNATFIGDHMKKGPTRPPRPGTPDLSKARDSPPASSNIVQGQIKQA   950
 951  AAPVSARSAADHSGSASASPALRTCFLVNEGWSQLAAMHCVMLPDLLGLG  1000
1001  KFRPPLLEMLARRWQDRCLEVREAAQALLLAELRRIEQAGRKETIDTWAP  1050
1051  YLPQYMDHVISPGVTAEAMQTMAAAPDASGPEAKVQEEEHDLVDDDITTG  1100
1101  CLSSVPQMKKMSTSYEERRKQATAIVLLGVIGAEFGAEIEPPKLLTRPRS  1150
1151  SSQIPEGFGLTSGGSNYSLARHTCKALTFLLLQPPSPKLPPHSTIRRTAI  1200
1201  DLIGRGFTVWEPYMDVSAVLMGLLELCADAEKQLANITMGLPLSPAADSA  1250
1251  RSARHALSLIATARPPAFITTIAKEVHRHTALAANTQSQQSIHTTTLARA  1300
1301  KGEILRVIEILIEKMPTDVVDLLVEVMDIIMYCLEGSLVKKKGLQECFPA  1350
1351  ICRFYMVSYYERSHRIAVGARHGSVALYDIRTGKCQTIHGHKGPITAVSF  1400
1401  APDGRYLATYSNTDSHISFWQMNTSLLGSIGMLNSAPQLRCIKTYQVPPV  1450
1451  QPASPGSHNALRLARLIWTSNRNVILMAHDGKEHRFMV              1488

Positively and negatively influencing subsequences are coloured according to the following scale:

(non-nuclear) negative ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| positive (nuclear)

with NucPred



If you find NucPred useful, please cite this paper:
NucPred - Predicting Nuclear Localization of Proteins. Brameier M, Krings A, Maccallum RM. Bioinformatics, 2007. PubMed id: 17332022
The authors also look forward to your comments and suggestions.

What does the NucPred score mean?

You have to decide on a NucPred score threshold. Sequences which score greater than or equal to this threshold are predicted to spend some time in the nucleus. Higher thresholds yield fewer predicted nuclear proteins, but these predictions are more accurate (you can have higher confidence in them). The table below gives more details of the performance of NucPred estimated using the sequences it was trained on (by cross-validation). Another benchmark is available in the Bioinformatics 2007 paper.

NucPred score threshold Specificity Sensitivity
see above fraction of proteins predicted to be nuclear that actually are nuclear fraction of true nuclear proteins that are predicted (coverage)
0.10 0.45 0.88
0.20 0.52 0.83
0.30 0.57 0.77
0.40 0.63 0.69
0.50 0.70 0.62
0.60 0.71 0.53
0.70 0.81 0.44
0.80 0.84 0.32
0.90 0.88 0.21
1.00 1.00 0.02

Sequences which score >= 0.8 with NucPred and which are predicted by PredictNLS to contain an NLS have been shown to be 93% correct with a coverage of 16%. (PredictNLS by itself is 87% correct with 26% coverage on the same data.)

Go back to the NucPred Home Page.